Mercurial > repos > proteomisc > preprocess_dataset

changeset 36:0aa849aec11e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author proteomisc
date Mon, 11 Dec 2023 19:37:42 +0000
parents 69a0a1cd02f5
children 10acbb8418d7
files preprocess_datasets/Affymetrix.Rmd
diffstat 1 files changed, 367 insertions(+), 51 deletions(-) [+]
line wrap: on
line diff
--- a/preprocess_datasets/Affymetrix.Rmd	Mon Dec 11 19:26:45 2023 +0000
+++ b/preprocess_datasets/Affymetrix.Rmd	Mon Dec 11 19:37:42 2023 +0000
@@ -1,57 +1,373 @@
-<!DOCTYPE html>
-<html lang="en">
-<head>
-    <meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
-    <title>Preprocessing Plots Before and After</title>
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="fr" lang="fr"><head>
+  <meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
+  <title>Preprocessing Plots Before and After</title>
+  <style>
+  /* css racine */
+
+body {
+/*  font-family: Comic Sans MS;*/
+}
+
+div.research {
+background-color: #33ffff; /*#208090 */ /*#228491*/;
+color: #0000ff; /* ffffff */
+}
+
+div.ensg {
+background-color: #bbee00;
+color: #0000ff;
+}
+
+div.research span.invisible {
+visibility:hidden;
+}
+
+kbd {
+color: #000000;
+}
+
+pre {
+color: #000000;
+}
+
+A:link {
+color: #0000ee; /*#ffffff;*/
+}
+
+A:active {
+color: #ff0000; /* #ffffff */
+}
+
+A:hover {
+/*  font-size: 2em; */
+text-decoration: none;
+color:  #0000ee; /* ffffff */
+background-color: #FFFF33;
+}
+
+h3 {
+color: #FF0000;
+}
+
+h4 {
+color: #FF0000;
+}
+
+div.correction {
+color: #008800;
+/*  color: #000000; */
+}
+
+div.detail {
+font-size: 70%;
+}
+
+div.section {
+text-align: center;
+font-size: 140%;
+color: #FF0000;
+}
+
+div.subsection {
+text-align: left;
+font-size: 120%;
+color: #bb0000;
+background-color: #FFFF33;
+}
+
+div.titreDuModule {
+text-align: center;
+font-size: 200%;
+color: #FF0099;
+}
+
+div.formation {
+text-align: center;
+font-size: 120%;
+color: #FF0099;
+}
+
+div.ensg.titreDuModule {
+text-align: center;
+font-size: 200%;
+color: #FF0099;
+}
+
+div.ensg.formation {
+text-align: center;
+font-size: 120%;
+color: #FF0099;
+}
+
+span.indice {
+font-size: 70%;
+}
+
+span.question {
+color: #bb0000;
+}
+
+span.tresImportant {
+color: #bb0000;
+font-size: 200%
+}
+
+span.assezImportant {
+color: #bb0000;
+font-size: 150%
+}
+
+span.important {
+color: #bb0000;
+}
+
+span.crucial {
+color: #bb0000;
+}
+
+span.crucial:hover {
+font-size: 400%;
+}
+
+acronym {
+text-decoration: none;
+}
+
+div.theoreme:before {
+content: "Théorème : ";
+}
+
+div.theoreme:after {
+content: "emèroéhT";
+}
+
+div.theoreme ul li:before {
+content: "1 alinéa ";
+}
+
+div.theoreme li:after {
+content: " ce qui termine l'alinéa";
+}
+
+div.tpID {
+background-color: #33ffff;
+color: #0000ff;
+}
+
+div.tpR {
+font-family: serif;
+color: #000000;
+background-color: #fff;
+}
+
+div.tpR span.detail {
+font-size: 75%;
+}
+
+div.tpR div.correction:before {
+content: "Idée de la correction : ";
+}
+
+div.tpR div.correction {
+background-color: #00ffff;
+border: solid #009999;
+padding: 0.5em;
+margin-left: 2em;
+border-width: 1px;
+}
+
+div.tpR div.exercices:before {
+content: "Exercices : ";
+}
+div.tpR div.exercices {
+background-color: #00ee00;
+border: solid #00cc00;
+padding: 0.5em;
+margin-left: 2em;
+border-width: 1px;
+}
+
+div.tpR div.solution:before {
+content: "Solution : ";
+}
+div.tpR div.solution {
+background-color: #ff00ff;
+border: solid #990099;
+padding: 0.5em;
+margin-left: 2em;
+border-width: 1px;
+}
+
+div.tpR div.exercice:before {
+content: "Exercice : ";
+}
+div.tpR div.exercice {
+background-color: #00ee00;
+border: solid #00cc00;
+padding: 0.5em;
+margin-left: 2em;
+border-width: 1px;
+}
+
+div.tpR div.questions:before {
+content: "Questions : ";
+}
+div.tpR div.questions {
+background-color: #ff99ff;
+border: solid #ff99ff;
+padding: 0.5em;
+margin-left: 2em;
+border-width: 1px;
+}
+
+div.tpR span.index {
+/*  background-color: #ffff33;*/
+}
+
+div.tpR h1 {
+font-family: sans-serif;
+color: #000;
+border-style: solid;
+background-color: #ddf;
+border-color: #88f;
+border-width: 1px;
+padding-left: 0.5em;
+}
+
+div.tpR h2 {
+font-family: sans-serif;
+color: #000;
+border-style: solid;
+border-color: #8f8;
+background-color: #dfd;
+border-width: 1px;
+padding-left: 0.5em;
+}
+
+div.tpR h3 {
+font-family: sans-serif;
+color: #000;
+border-style: solid;
+background-color: #fdd;
+border-color: #f88;
+border-width: 1px;
+padding-left: 0.5em;
+}
+
+div.tpR a:link {
+color: #00f
+}
+
+div.tpR a:visited {
+color: #f0f
+}
+
+div.tpR p {
+margin-left: 1em;
+}
+
+div.tpR pre {
+background-color: #eee;
+border: solid #ccc;
+padding: 0.5em;
+margin-left: 2em;
+border-width: 1px;
+}
+
+.redify pre {
+color: #ff0000;
+}
+
+div.tpR hr {
+border-style: solid;
+border-color: #02c;
+background-color: #ddf;
+border-color: #88f;
+border-width: 1px;
+padding-top: 1px;
+padding-bottom: 1px;
+}
+
+div.pp {
+color: #FF0000;
+}
+
+div.infobulle{
+position: absolute;
+visibility : hidden;
+border: 1px solid Black;
+padding: 10px;
+font-family: Verdana, Arial;
+font-size: 13px;
+background-color: #ffffff;
+-moz-border-radius: 20px; /* pour avoir des coins arrondis */
+}
+
+/* http://www.w3schools.com/CSS/css_display_visibility.asp */
+span.commentPub{
+background-color: #77ff33;
+}
+
+span.moreCommentOnPub{
+/*  position: absolute;*/
+/*  visibility : hidden;*/
+/*  border: 1px solid Black;
+padding: 10px;
+font-family: Verdana, Arial;
+font-size: 13px;*/
+background-color: #77ff33;
+-moz-border-radius: 3em 1em /* 20px; pour avoir des coins arrondis */
+border-radius: 3em 1em; /* 20px; pour avoir des coins arrondis */
+}
+</style>
 </head>
 <body>
 <div class="tpR">
-    <h1>Preprocessing</h1>
-    <p>
-        Preprocessing of an `r datasetsource` DataSet, issued from
-        `r technology`
-        technology.
-    </p>
-    <h2>Used methods for each step</h2>
+<h1>Preprocessing</h1>
+<p>
+Preprocessing of an `r datasetsource` DataSet, issued from
+`r technology`
+technology.
+</p>
+<h2>Used methods for each step</h2>
 
-    <h3>Background correction methods</h3>
-    <pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
-    <h3>Normalization methods</h3>
-    <pre>method : `r listArguments[["normalization_method"]]`</pre>
-    <h3>Summarization methods</h3>
-    <pre>method : `r listArguments[["summary_method"]]`</pre>
-    <h2>Boxplots</h2>
-    <h3>Before NM</h3>
-    <p>
-        <br>
-        <img src="boxplot_before_NM.png" width="100%" height="auto" alt="">
-        <br>
-    </p>
-    <h3>After NM</h3>
-    <p>
-        <br>
-        <img src="boxplot_after_NM.png" width="100%" height="auto" alt="">
-        <br>
-    </p>
-    <h2>MA plots</h2>
-    <p>
-        <br>
-        <img src="MA_plot.png" width="100%" height="auto" alt="">
-        <br>
-    </p>
-    <h2>Densities plot</h2>
-    <h3>Before NM</h3>
-    <p>
-        <br>
-        <img src="densities_plot_before_NM.png" width="100%" height="auto" alt="">
-        <br>
-    </p>
-    <h3>After NM</h3>
-    <p>
-        <br>
-        <img src="densities_plot_after_NM.png" width="100%" height="auto" alt="">
-        <br>
-    </p>
-</div>
+<h3>Background correction methods</h3>
+<pre>method : `r listArguments[["backgroundcorrection_method"]]`</pre>
+<h3>Normalization methods</h3>
+<pre>method : `r listArguments[["normalization_method"]]`</pre>
+<h3>Summarization methods</h3>
+<pre>method : `r listArguments[["summary_method"]]`</pre>
+<h2>Boxplots</h2>
+<h3>Before NM</h3>
+<p>
+<br>
+<img src="boxplot_before_NM.png" width="100%" height="auto">
+<br>
+</p>
+<h3>After NM</h3>
+<p>
+<br>
+<img src="boxplot_after_NM.png" width="100%" height="auto">
+<br>
+</p>
+<h2>MA plots</h2>
+<p>
+<br>
+<img src="MA_plot.png" width="100%" height="auto">
+<br>
+</p>
+<h2>Densities plot</h2>
+<h3>Before NM</h3>
+<p>
+<br>
+<img src="densities_plot_before_NM.png" width="100%" height="auto">
+<br>
+</p>
+<h3>After NM</h3>
+<p>
+<br>
+<img src="densities_plot_after_NM.png" width="100%" height="auto">
+<br>
+</p>
 </body>
 </html>
\ No newline at end of file